When I researched this before I couldn't find anything that let you apply MP3Gain type alterations to FLAC files. The changes MP3Gain makes are preserved in tags and can be reversed. After MP3Gain reverses the changes the audio information is exactly the same as before the changes.

Being able to make a lossless change to the volume levels that way is part of what makes it useful. If you ever change your mind MP3Gain can reverse the changes using the tags it's written and you have the exact same audio information as before.

When I looked for a tool that did the same thing to FLAC files I came up empty. The closest thing I found that you can apply Replaygain during conversion to alter the files using foobar2000's Converter. The changes made that way are permanent. That also means the files are no longer lossless. The audio information isn't the same as the original so it wouldn't be considered lossless.